I have a dell optiplex 990, that's about a month old, running Fedora 16, Gnome 3. Something happened where it wouldn't turn on anymore, Dell sent me a new motherboard, and now it boots fine, and the keyboard works just fine in bios and for selecting boot options, but when I get to the login screen, pressing any key causes the screen to flash, but nothing is typed. The crazy thing is, even the onscreen keyboard has the same problem.

The keyboard works in another computer, and other keyboards have the same issue in this one, and if I boot under recovery mode, or use a live cd, the keyboard works just fine. I can ssh into the computer and use the terminal just fine. The mouse also works without any issues. Once I get to the boot screen, though, the keyboard stops working.

I really don't want to have to re-install the OS, because I have a lot of research software I don't wan't to have to re-install.

Any ideas? This is crazy!

Update: If I hold a key down, the screen flashes twice, then that keypress is registered. I can repeat this to enter my password, then once I login, the keyboard works normally.

Have a look at your "grub" configuration.
Also, is your hard disk encrypted ?

Upon your suggestion, I tried reinstalling grub, but that didn't fix the problem, unfortunately.

The hard drive is not encrypted. I can take the drive out and put it in another identical computer, and it has the same problem, and I can take another hard drive with the same OS and put it in this, and it works fine, which I think means something happened to some system file(s) somewhere?

I'll bet the BIOS on the old main board was different than the one now, assuming you did the install on the old board.

Perhaps copy : /boot/grub2/grub.cfg folder from the HD that works, and also the X keyboard config: /etc/X11/xorg.conf to a thumb drive, then reinstall the problem drive. Compare the files using "diff" if you are comfortable with the command line, or there is a really neat little program called "meld" which can show you the differences in the files graphically. Whatever method, compare the files.

If that shows you nothing, then look at the Ibus setup, from the command line : ibus-setup

The rational is that kernel options are loaded at boot ( in grub ), and then passed along to the X window system. Somewhere along the way ( I think between grub and X ) Ibus gets involved.

Make sure your BIOS is the latest. If you still have the old main board around, see if you can spot the BIOS version on it.

Let me know. I love a good mystery !